Align N-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate PfGW456L13_4833 PTS system, N-acetylglucosamine-specific IIA component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIB component (EC 2.7.1.69) / PTS system, N-acetylglucosamine-specific IIC component (EC 2.7.1.69)
Query= reanno::pseudo3_N2E3:AO353_04465 (571 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4833 Length = 571 Score = 993 bits (2566), Expect = 0.0 Identities = 495/571 (86%), Positives = 534/571 (93%) Query: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLALIFAI 60 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLA+IFAI Sbjct: 1 MYQLFIEGLQRLGRALMLPIAILPIAGLLLRLGDTDLLNIAIIHDAGQVIFANLAMIFAI 60 Query: 61 GIAVGFARDNNGTAGLAGAIGYLVMVSTLKVLDASINMGMLAGIISGLMAGALYNRFKDI 120 GIAVGFARDNNGTAGLAG IGYLVM+STLK LD SINMGMLAGI+SGLMAGALYNRFKDI Sbjct: 61 GIAVGFARDNNGTAGLAGVIGYLVMISTLKALDPSINMGMLAGIVSGLMAGALYNRFKDI 120 Query: 121 KLPEYLAFFGGRRFVPIATGFSAVGLGVIFGLIWPPIQHGINSFGQLLLESGSIGAFVFG 180 KLPEYLAFFGGRRFVPI TGF+AVGLGV+FG IWPPIQHGINSFG L++ESGS GAFVFG Sbjct: 121 KLPEYLAFFGGRRFVPIVTGFAAVGLGVVFGYIWPPIQHGINSFGTLMMESGSFGAFVFG 180 Query: 181 VFNRLLIVTGLHHILNNMAWFIFGSFTDPTTGAIVTGDLARYFAGDPKGGQFMTGMFPMM 240 +FNRLLIVTGLHHILNNMAWF+FG+FTDPTTGA+VTGDL+RYFAGDPKGGQFMTGMFPMM Sbjct: 181 LFNRLLIVTGLHHILNNMAWFVFGNFTDPTTGALVTGDLSRYFAGDPKGGQFMTGMFPMM 240 Query: 241 IFGLPAACLAMYRNALPERRKVMGGIFLSMALTSFLTGVTEPIEFAFMFLAPLLYLLHVL 300 IFGLPAACLAMYRNALP RRKVMGGIFLSMALT+FLTGVTEPIEFAFMFLAPLL++LH L Sbjct: 241 IFGLPAACLAMYRNALPARRKVMGGIFLSMALTAFLTGVTEPIEFAFMFLAPLLFVLHAL 300 Query: 301 LTGMAMAITNALNIHLGFTFSGGAIDMALGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360 LTG++MAITNALNIHLGFTFSGG IDM LGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR Sbjct: 301 LTGLSMAITNALNIHLGFTFSGGFIDMILGWGKSTNGWLVFPVGLAYAVIYYVVFDFCIR 360 Query: 361 RFNLKTPGREGVVVGEKVVLSENQRAGAYIQALGGAENLITVGACTTRLRLEMVDRNKAS 420 RF+LKTPGRE E+V +++N+RAGAYI+ALGGAENLITVGACTTRLRL+MVDRNKAS Sbjct: 361 RFDLKTPGRETSADVEQVAVADNERAGAYIKALGGAENLITVGACTTRLRLDMVDRNKAS 420 Query: 421 DSELKALGAMAVVRPGKGGSLQVVVGPLADSIADEIRQAMPTAGSALVAAVVVTEEAPKA 480 D++LKALGAMAVVRPGKGGSLQVVVGP+AD+IADEIR AMP G A+V++ +AP Sbjct: 421 DTDLKALGAMAVVRPGKGGSLQVVVGPMADAIADEIRLAMPALGRAMVSSPAAEIDAPPP 480 Query: 481 APVETPEAQKWLNAVGGSDNVLQLDCVAMTRIRLQLADGKALSECQLKDLGCQGVSALDG 540 A + TPEAQ+WLNA+GG DNVLQLDCVAMTRIRLQLADGKALSE LK LGCQGVS LDG Sbjct: 481 AAMATPEAQQWLNALGGGDNVLQLDCVAMTRIRLQLADGKALSEFDLKALGCQGVSQLDG 540 Query: 541 GVWHLLIGDKALSLSEALEGLVNRSEVSAKV 571 G+WHLLIGDKA +LS+ALE LVNRSEVSAKV Sbjct: 541 GIWHLLIGDKAPTLSDALEVLVNRSEVSAKV 571 Lambda K H 0.325 0.142 0.421 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1190 Number of extensions: 53 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 571 Length of database: 571 Length adjustment: 36 Effective length of query: 535 Effective length of database: 535 Effective search space: 286225 Effective search space used: 286225 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory